clausevitz, jomini, study them. To even ask the question of explaining morality in war suggests you might have thought there should be morality in war. I am sorry you got that impression. A short essay on my thoughts and others:
War is an extension of politics - clausevitz. In the quest to get some power/people/entity to stop doing something (invading, destabilizing, living in some land you want) you must find a way (a policy) that convinces them (harasses them) such that continued pursuit of the policy you abhor (invading, destabilizing, living in some land you want) is NOT in their best interests. Since kings/presidents/governments tend to listen to their people _before_ they listen to some other king/president/government - your task as a war strategist: convince the king/president/government to stop the behavior you abhor (invading, destabilizing, living in some land you want) by causing chaos and fear amongst his population (the people who pay for the invading, destabilizing, living in some land you want activities). This could be peaceful (voice of america), cruel (trade emabargoes, sanctions), or violent (killing them / breaking their stuff until they see your way)
Jomeni advocated bombing the city centers (al queda have you been studying jomeni?) to cause chaos.
This method of warfare dominated US strategy during WW2 (nagasaki, hiroshima, fire bombings: germany, japan) and briefly during linebacker 2 of the vietnam war.
This is also the method of warfare of "terrorists" since beirut. Using largely ineffective, but spectactular effects to scare people. (cars/heart attacks/cancer kill way many more people than terrorists)
Recent glamorization of war (going back as far as the chivalry movement of the knights to cut down on the sheer barbarism of war) since WW2 has led to this thought of "civilians" - people who have nothing to do with war - and thus don't deserve to be targeted: it is merely a myth to calm the palettes of doves to convince them that war isn't really all that bad. Which of course is not true.
Once we stop the idea of "civilian" - I think people will realize that we all are responsible for the people we put in office, and it is our responsibility to stop them from expressing anything other than our intent when it comes to war. we are all in this fight, whether it be school teachers educating the next marines, or even the grocery store, our taxes fund the war machine and are a collective message to the rest of the world on our approval of the current war we are in.
in short: war was never meant to be moral - it is simply getting a country to do something they do not want to do, by means of strategic maneuvering (bombs, trade, money, isolation, invasion, eradication)